Characterizing cultivable soil microbial communities from copper fungicide-amended olive orchard and vineyard soils

World Journal of Microbiology and Biotechnology

Volumn 24, Issue 3, 2008, Pages 309-318

  Viti, Carlo ^a   Quaranta, Davide ^a,b   De Philippis, Roberto ^a   Corti, Giuseppe ^c   Agnelli, Alberto ^c   Cuniglio, Rosanna ^c   Giovannetti, Luciana ^a  

^a UNIVERSITY OF FLORENCE   (Italy)

^b UNIVERSITY OF ARIZONA   (United States)

^c UNIVERSITÀ POLITECNICA DELLE MARCHE   (Italy)

Author keywords

ARDRA; CLPP Biolog; Copper; Copper fractionation; Microbial community

Indexed keywords

DNA; FUNGICIDES; SOILS;

COPPER FRACTIONATION; MICROBIAL COMMUNITY; OLIVE ORCHARD;

MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 39649088979     PISSN: 09593993     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11274-007-9472-x     Document Type: Article

References (44)

1. Bååth E (1989) Effects of heavy metals in soil on microbial processes and populations. Water Air Soil Pollut 64:627-633
2. Berna F, Corti G, Ugolini FC, Agnelli A (2000) Assessment of the role of rock fragments in the retention of cadmium and lead in irrigated arid stony soils. Ann Chim 90:209-217
3. Borneman J, Skroch PW, O'Sullivan KJ, Palus JA, Rumjanek NG, Jansen JL, Nienhuis J, Triplett EW (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62:1935-1943
4. Brandt KK, Petersen A, Holm PE, Nybroe O (2006) Decreased abundance and diversity of culturable Pseudomonas spp. populations with increasing copper exposure in the sugar beet rhizosphere. FEMS Microbiol Ecol 56:281-291
5. Brookes PC (1995) The use of microbial parameters in monitoring soil pollution by heavy metals. Biol Fertil Soils 19:269-279
6. Cho JC, Kim SJ (2000) Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input. Appl Environ Microbiol 66:956-965
7. + -N. Eur J Soil Sci 50:523-534
8. Day PR (1965) Particle fractionation and particle-size analysis. In: Black CA, Evans DD, Ensminger LE, White JL, Clarck FE (eds) Methods of soil analysis. American Society of Agronomy, Madison, Wisconsin, pp 545-567
9. Deluisa A, Giandon P, Aichner M, Bortolami P, Bruna L, Lupetti A, Nardelli F, Stringari G (1996) Copper pollution in Italian vineyard soils. Commun Soil Sci Plant Anal 27:1537-1548
10. Doelman P, Jansen A, Michelis M, van Til M (1994) Effects of heavy metals in soil on microbial diversity and activity as shown by the sensitivity-resistance index, an ecologically relevant parameter. Biol Fertil Soils 17:177-184
11. Dumestre A, Sauvé S, McBride M, Baveye P, Berthelin J (1999) Copper speciation and microbial activity in long-term contaminated soils. Arch Environ Contam Toxicol 36:124-131
12. Eijsackers H, Beneke P, Maboeta M, Louw JPE, Reinecke AJ (2005) The implications of copper fungicide usage in vineyards for earthworm activity and resulting sustainable soil quality. Ecotoxicol Environ Saf 62:99-111
13. El Fantroussi S, Verschuere L, Verstraete W, Top EM (1999) Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl Environ Microbiol 65:982-988
14. Ellis RJ, Thompson IL, Bailey MJ (1995) Metabolic profiling as means of characterizing plant-associated microbial communities. FEMS Microbiol Ecol 16:9-18
15. Franklin RB, Garland JL, Bolster CH, Mills AL (2001) Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments. Appl Environ Microbiol 67:702-712
16. Frostegård Å, Courtois S, Ramisse V, Clerc S, Bernillon D, Le Gall F, Jeannin P, Nesme X, Simonet P (1999) Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol 65:5409-5420
17. Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl Environ Microbiol 57:2351-2359
18. Gauch HG (1982) Multivariate analysis in community ecology. Cambridge University Press, Cambridge
19. Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69:1800-1809
20. Huysman F, Verstraete W, Brookes PC (1994) Effect of manuring practices and increased copper concentration on soil microbial populations. Soil Biol Biochem 26:103-110
21. Insam H, Goberna M (2004) Use of Biolog for the community level physiological profiling (CLPP) of environmental samples. In: Akkermans ADL, van Elsas DJ, de Bruij FJ (eds) Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, pp 1-8
22. Killham K (1994) Soil ecology. Cambridge University Press, Cambridge
23. Konopka A, Oliver L, Turco RFJR (1998) The use of carbon substrate utilization patterns in environmental and ecological microbiology. Microb Ecol 35:103-115
24. Konopka A, Zakharova T, Bischoff M, Oliver L, Nakatsu C, Turco RF (1999) Microbial biomass and activity in lead-contaminated soil. Appl Environ Microbiol 65:2256-2259
25. Kunito T, Saeki K, Oyaizu H, Matsumoto S (1999) Influences of copper forms on the toxicity to microorganisms in soils. Ecotox Environ Saf 44:174-181
26. Marschner P, Kandeler E, Marschner B (2003) Structure and function of the soil microbial community in a long-term fertilizer experiment. Soil Biol Biochem 35:453-461
27. McLeod S (1975) Studies on wet oxidation procedure for determination of "organic C" in soil. In: Notes in soil techniques. CSIRO Division of Soil, Adelaide, pp 73-79
28. Mergeay M (1995) Heavy metal resistances in microbial ecosystems. In: Akkermans ADL, van Elsas DJ, de Bruij FJ (eds) Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, pp 1-17
29. O'Donnell AG, Goodfellow M, Hawksworth DL (1994) Theoretical and practical aspects of the quantification of biodiversity among microorganisms. Philos Trans R Soc London Ser B 345:65-73
30. Pielou EC (1966) The measurement of diversity in different types of biological collections. J Theoret Biol 13:131-144
31. Pietrzak U, McPhail DC (2004) Copper accumulation, distribution and fractionation in vineyard soils of Victoria, Australia. Geoderma 122:151-166
32. Sayler GS, Shields MS, Tedford ET, Breen A, Hooper SW, Sirotkin KM, Davis JW (1985) Application of DNA-DNA hybridization to the detection of catabolic genotypes in environmental samples. Appl Environ Microbiol 49:1295-1303
33. Shannon CE, Weaver W (1963) The mathematical theory of communication. University of Illinois Press, Urbana
34. Singh BK, Millard P, Whiteley AS, Murrell JC (2004) Unravelling rhizosphere-microbial interactions: opportunities and limitations. Trends Microbiol 8:386-393
35. Skoog S, West D (1987) Analytical chemistry: an Introduction. WB Saunders Co. Publisher, Philadelphia, USA
36. Smit E, Leeflang P, Wernars K (1997) Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiol Ecol 23:249-261
37. Soil Survey Staff (2003) Keys to soil taxonomy. USDA, NRCS Publishers, Washington DC, p 326
38. Stephan A, Meyer AH, Schmid B (2000) Plant diversity affects culturable soil bacteria in experimental grassland communities. J Ecol 88:988-998
39. Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240-245
40. Verschuere L, Fievez V, Van Vooren L, Verstraete W (1997) The contribution of individual population to the Biolog pattern of model microbial communities. FEMS Microbiol Ecol 24:353-362
41. Viti C, Giovannetti L (2001) The impact of chromium contamination on soil heterotrophic and photosynthetic microorganisms. Ann Microbiol 51:201-213
42. Viti C, Giovannetti L (2005) Characterization of cultivable heterotrophic bacterial communities in Cr-polluted and unpolluted soils using Biolog and ARDRA approaches. Appl Soil Ecol 28:101-112
43. Viti C, Mini A, Ranalli G, Lustrato G, Giovannetti L (2006) Response of microbial communities to different doses of chromate in soil microcosms. Appl Soil Ecol 34:125-139
44. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697-703